python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Input-GSM2186473/*_1.fastq.gz Input-GSM2186473/*_2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Input-GSM2186473/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Rep1-WG-STARR-seq-GSM2186474/*_1.fastq.gz Rep1-WG-STARR-seq-GSM2186474/*_2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Rep1-WG-STARR-seq-GSM2186474/alignments.2x36mers.unique
python /oak/stanford/groups/akundaje/marinovg/code/PEFastqToTabDelimited.py Rep2-WG-STARR-seq-GSM2186475/*_1.fastq.gz Rep2-WG-STARR-seq-GSM2186475/*_2.fastq.gz -trim 36 36 | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/hg19/bowtie-indexes/hg19-female -p 8 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh -X 1000 --sam --12 - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/hg19/sequence/hg19.fa - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools sort - Rep2-WG-STARR-seq-GSM2186475/alignments.2x36mers.unique